Programming molecular topologies from single-stranded nucleic acids

• Published in: Nature communications 2018-11, Vol.9 (1), p.4579-9, Article 4579
• Main Authors: Qi, Xiaodong, Zhang, Fei, Su, Zhaoming, Jiang, Shuoxing, Han, Dongran, Ding, Baoquan, Liu, Yan, Chiu, Wah, Yin, Peng, Yan, Hao
• Format: Article
• Language: English
• Subjects: 147/28; 147/3; 38/22; 38/90; 60 APPLIED LIFE SCIENCES; 639/301/54/992; 639/925/926/1049; 639/925/926/1051; Cryoelectron Microscopy; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - ultrastructure; Humanities and Social Sciences; Knots; Microscopy, Atomic Force; multidisciplinary; Nanostructure; Nucleic Acid Conformation; Nucleic acids; Nucleic Acids - chemistry; Nucleotides; Polymers; Ribonucleic acid; RNA; RNA - chemistry; Science; Science (multidisciplinary); Single-stranded DNA; Topology
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-07039-7

Molecular knots represent one of the most extraordinary topological structures in biological polymers. Creating highly knotted nanostructures with well-defined and sophisticated geometries and topologies remains challenging. Here, we demonstrate a general strategy to design and construct highly knotted nucleic acid nanostructures, each weaved from a single-stranded DNA or RNA chain by hierarchical folding in a prescribed order. Sets of DNA and RNA knots of two- or three-dimensional shapes have been designed and constructed (ranging from 1700 to 7500 nucleotides), and they exhibit complex topological features, with high crossing numbers (from 9 up to 57). These single-stranded DNA/RNA knots can be replicated and amplified enzymatically in vitro and in vivo. This work establishes a general platform for constructing nucleic acid nanostructures with complex molecular topologies. Designing nucleic acid-based nanostructures with knots remains challenging. Here the authors present a general strategy to design and construct highly knotted 2D and 3D nanostructures from single-stranded DNA or RNA